School on "Biomolecular Simulations"
Lecture Notes and Tutorials
Day 1 Nov 6, 2007
- Biomolecular simulation
- DNA structure and dynamics (Manju Bansal)
- Introduction to Protein Structure folding and Dynamics (Saraswathi Vishveshwara )
- Tutorial
Day 2 Nov 7, 2007
- Extended system molecular dynamics (Balasubramaniam Sundaram)
- Reversible integrators and multiple time step method (Balasubramaniam Sundaram)
- Scripting wiht TCL, Part - I(Axel Kohlmeyer)
- Tutorial
Day 3 Nov 8, 2007
- Introduction to simulation methodologies(Srikanth Sastry)
- Scripting wiht TCL, Part - II(Axel Kohlmeyer)
- Tutorial
Day 4 Nov 9, 2007
- Introduction to Force Fields(Vani Vemparala)
- Length and Time scale issues in Molecular simulation(Prabal K Maiti)
- Tutorial
Day 5 Nov 10, 2007
- Ewald and Particle Mesh Ewald and Cell Multipole method(Prabal K Maiti)
- Getting Help with VMD & VMD Command Line Flags(Axel Kohlmeyer)
- Tutorial
Day 6 Nov 12, 2007
- Constraints and Langevin dynamics(Srikanth Sastry)
- Advanced VMD Script Examples and Customization (Axel Kohlmeyer)
- Tutorial
Day 7 Nov 13, 2007
- Membranes & Membrane Proteins (Vani Vemparala)
- Coarse grained simulations of Lipid Bilayer Membranes(P.B.Sunil Kumar)
- Coarse Grained MD Parametrization and Application to Peptide Nanotube Formation (Axel Kohlmeyer)
- Tutorial
Day 8 Nov 14, 2007
- Dissipative Particle Dynamics Simulations of Multi-Component Fluids(P.B.Sunil Kumar)
- Nucleic Acid Structure Analysis(Dhananjay Bhattacharyya and Manju Bansal)
- Dynamics of Nucleic Acids Analyzed from Base Pair Geometry(Dhananjay Bhattacharyya)
- Tutorial
Day 9 Nov 15, 2007
- Free Energy Methods(Srikanth Sastry)
- Correlated Movements in Proteins: Insights from the Dynamics of Protein Structure Networks( Saraswathi Vishveshwara)
- Tutorial